[2024-01-24 14:14:36,183] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:36,184] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:36,185] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0b70ea9-9446-4ee5-9014-b68aee90533f/dqc_reference
[2024-01-24 14:14:38,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:38,816] [INFO] Task started: Prodigal
[2024-01-24 14:14:38,816] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8eff689-dfa5-4b0d-9e27-2df6a55e436d/GCF_009728735.1_ASM972873v1_genomic.fna.gz | prodigal -d GCF_009728735.1_ASM972873v1_genomic.fna/cds.fna -a GCF_009728735.1_ASM972873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:56,842] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:56,843] [INFO] Task started: HMMsearch
[2024-01-24 14:14:56,843] [INFO] Running command: hmmsearch --tblout GCF_009728735.1_ASM972873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0b70ea9-9446-4ee5-9014-b68aee90533f/dqc_reference/reference_markers.hmm GCF_009728735.1_ASM972873v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:57,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:57,173] [INFO] Found 6/6 markers.
[2024-01-24 14:14:57,227] [INFO] Query marker FASTA was written to GCF_009728735.1_ASM972873v1_genomic.fna/markers.fasta
[2024-01-24 14:14:57,228] [INFO] Task started: Blastn
[2024-01-24 14:14:57,229] [INFO] Running command: blastn -query GCF_009728735.1_ASM972873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0b70ea9-9446-4ee5-9014-b68aee90533f/dqc_reference/reference_markers.fasta -out GCF_009728735.1_ASM972873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:58,268] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:58,272] [INFO] Selected 12 target genomes.
[2024-01-24 14:14:58,272] [INFO] Target genome list was writen to GCF_009728735.1_ASM972873v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:58,277] [INFO] Task started: fastANI
[2024-01-24 14:14:58,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8eff689-dfa5-4b0d-9e27-2df6a55e436d/GCF_009728735.1_ASM972873v1_genomic.fna.gz --refList GCF_009728735.1_ASM972873v1_genomic.fna/target_genomes.txt --output GCF_009728735.1_ASM972873v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:12,394] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:12,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0b70ea9-9446-4ee5-9014-b68aee90533f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:12,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0b70ea9-9446-4ee5-9014-b68aee90533f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:12,411] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:12,411] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:12,412] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	86.4732	1516	1903	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	83.1441	1059	1903	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	83.0619	1070	1903	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	82.8445	1146	1903	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	82.6906	1138	1903	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	82.5633	974	1903	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	81.1953	754	1903	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	80.8403	854	1903	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	80.0032	700	1903	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.0463	550	1903	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	78.6627	506	1903	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	78.5329	507	1903	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:12,413] [INFO] DFAST Taxonomy check result was written to GCF_009728735.1_ASM972873v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:12,414] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:12,414] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:12,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0b70ea9-9446-4ee5-9014-b68aee90533f/dqc_reference/checkm_data
[2024-01-24 14:15:12,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:12,479] [INFO] Task started: CheckM
[2024-01-24 14:15:12,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009728735.1_ASM972873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009728735.1_ASM972873v1_genomic.fna/checkm_input GCF_009728735.1_ASM972873v1_genomic.fna/checkm_result
[2024-01-24 14:16:05,078] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:05,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:05,110] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:05,111] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:05,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009728735.1_ASM972873v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:05,112] [INFO] Task started: Blastn
[2024-01-24 14:16:05,112] [INFO] Running command: blastn -query GCF_009728735.1_ASM972873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0b70ea9-9446-4ee5-9014-b68aee90533f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009728735.1_ASM972873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:07,797] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:07,801] [INFO] Selected 8 target genomes.
[2024-01-24 14:16:07,801] [INFO] Target genome list was writen to GCF_009728735.1_ASM972873v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:07,809] [INFO] Task started: fastANI
[2024-01-24 14:16:07,809] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8eff689-dfa5-4b0d-9e27-2df6a55e436d/GCF_009728735.1_ASM972873v1_genomic.fna.gz --refList GCF_009728735.1_ASM972873v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009728735.1_ASM972873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:18,769] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:18,818] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:18,819] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000468095.1	s__Pantoea sp000468095	98.4986	1555	1903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.52	98.52	0.95	0.95	2	conclusive
GCF_000175935.2	s__Pantoea sp000175935	90.0833	1657	1903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095535.1	s__Pantoea cypripedii	86.4555	1519	1903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
GCF_011395035.1	s__Pantoea cypripedii_A	86.4333	1484	1903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014155765.1	s__Pantoea dispersa	83.0597	1070	1903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.93	96.36	0.92	0.86	38	-
GCF_001187905.1	s__Pantoea sp001187905	82.6458	1119	1903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCA_900215435.1	s__Pantoea sp900215435	82.5687	1091	1903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.51	99.02	0.98	0.96	3	-
GCF_007833795.1	s__Pantoea dispersa_B	82.3899	974	1903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:18,820] [INFO] GTDB search result was written to GCF_009728735.1_ASM972873v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:18,821] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:18,825] [INFO] DFAST_QC result json was written to GCF_009728735.1_ASM972873v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:18,825] [INFO] DFAST_QC completed!
[2024-01-24 14:16:18,825] [INFO] Total running time: 0h1m43s